1Y4D

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59R/E60S mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TM3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5277potassium phosphate, PEG 8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.345.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.381α = 90
b = 115.381β = 90
c = 42.907γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.000ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1232.5599.60.1577.44.92216022160-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TM3232.552215621026113099.160.199960.199960.19710.25207inherited from 1TM326.581
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.52-0.26-0.520.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.881
r_scangle_it4.393
r_scbond_it2.783
r_mcangle_it1.826
r_angle_refined_deg1.81
r_mcbond_it1.088
r_symmetry_hbond_refined0.301
r_nbd_refined0.219
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.881
r_scangle_it4.393
r_scbond_it2.783
r_mcangle_it1.826
r_angle_refined_deg1.81
r_mcbond_it1.088
r_symmetry_hbond_refined0.301
r_nbd_refined0.219
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.166
r_chiral_restr0.131
r_metal_ion_refined0.083
r_bond_refined_d0.023
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2461
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms2

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling